Gene detail

Detailed information of evm.model.HiC_scaffold_32.210 in Chrysaora quinquecirrha

Genomic Location: HiC_scaffold_32:2583544...2605443
NR annotation: XP_047135748.1, nonsense-mediated mRNA decay factor SMG7 [Hydra vulgaris]
Species Chrysaora quinquecirrha · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

evm.model.HiC_scaffold_32.210

AtgagttatgtttattgcttttttagGCAAGCAGAAGGCTTAAAAGCAAACATTTCAGGGAAATTTGCTGAAGCCACTGATTTTTTCTCTGAAGAATTTGTAACATGTAAAAACCTTCAAGACATTTATAAGACAATTTTGCTATCTGACTTGCAGTATGCACTGGATAGGAAAGTTGAGCTTGAGCTATGGAACAATGCATTTAAATGCCATATTGACTACCTGAGACAACGCTTGAAAGCAAAAAAGGGCTCTGAGAAGGCTGCATTGCAAGCAAAATTAACATTCTTGATTGATGCCACCATGGGCTTTTACTTGCAGCTACTTGAAGAATTTTGCGATCATAATGACCTCGAGTCACCTTTTCTCAAGAAAGCACTGGCCCTTGATCTTATACCTGAGTATAATGGGTTGGAAGCAGAGCAAAAAGATAAGCCGAAAGCTAGTTCTTGTTATTATGTCTGCCAAGACTGCCTGGTTCATCTTGGAGATCTCGCTCGATACAAGAATGACACTAATCAAGCGGAATCCTATTACAAGATGGCGTCAAAAGTCGTTGCTGTAAATGGTCAACCATACAATCAGCTTGCCATAATCGCCAGCTCAAAAGGAGATCAACTCAAAGCTGTTTTCTATTATTGTAAAAGTGTTTTGGTTCAGAATCCGTTTCCCGCTGCCGTTTCGAATTTGCAGAAGACTTTTAATCAATTTTGCTCAAGACAAAGTCTCGGTGTTTTGACCAAAAGCAGTTCTTCGTCTGTAGATGAGTTTATCTCTCTCTTTCTGCTGTATCATGGTTCGGTATACCTAATGCACAATGTTGATAAACTTTCAAAGATTCAAGAGAGAATACTAGCCGACTTTGACGACATTCATGAAGACCTAACTAATGACCAATTATTCCACTTGactgttttgaacattttcacaatttacaaaaacaaaCCCAAAGAAGATGACGAACAAGACGACTGCATCGCAGATGACGAAATTGAGGTCTGGAATCTAGTCATCGCTTTCACCTTGTCGTTTTACGGTTGCTTAGTAACGCTTGCTGTTTCGCTGTTTGATACTGAAGACGAGGCTAATGCTGAGAGATTTCTGCCGAGCATCAAGGTCTTATCTGATTTCATTCTGTGCAGTGGTTCGTCAATATTGATGCAGAAGGCCTTCGAGGATAATGTTGAGCCTATATCTACACCAACAGtcatgattatgattatgcctATGTGTATGACACGATTGAAATTATTCTTCCTTACAGCCATTCCTCTTCCGGAAGACCATGAAATCAATGGCTTCTTTCCTCTAAGAAGAATTCACAGGAAACTAGACTtcaaagaaaaggaaatttcagaagaaaacACCAAATCACTAAGAGCATACCGCATCATTTCATTTATAAACTGGTTGTGTCAGCAAGAACCGGCTTCAAGGTATATCGGTAAAGGTGAACGTGAAGGCGAGGCTCGATTCATTTGCCTGCAAGGTGAAGCAGCAAAAGACGAAGCCACAGCTGCCGAAGATTGCAGAATGAGTGATAAAGATTTCGATGTCGCACTTAGAAAACTTTTTGATGCATTACCTGAACTTCACGTGTTGATTGTCATCAATGATGCAAAAGGGGACTTGGCTGGAAAGGGATTATTCATGAATAAATCTACAAACATAAGAGAAGGTGAAGAAGATTGTCTGGTTGGTAGGCAGAGATTTGAAGGGATTAAGGAGTTAGAAACAGCGATGGTTAATAACGAAGATAAATCAAATAGCCTGGCAGCTAATGGCAGAGGAAACGCAACAATTGGCAAGCTTAAAATGCCAGAAAAGTTTGCAAATGTTGGTGGAAACAGTGGTCAGAGAAAAGACTTAGGTAACAGACAGAAAGGTACTCGACTGAGCGAAAAAGGCTTTGAAGGCAACAAGGGAATCGTTAGTACCGCGGCTAGTAATTCTAATCGGAGAAGTGGGAGAGAGAACAGccagaaaatcaatgaaaataaagattctGAAGGCAGCAAGGGAATCGCCTGCGACGGGGCTACTAATACTAAAAAACAGAGTGACTTTGCTGTGAAACAAAATGGTGGTAAAGTCAACGAGAATCAACGCTCTCAAGGTAGCCGGGGAATCTTCAACGCTGAAGCATCAAAGAGTCCAATTCAAGAATCCATGAAGAAGTTCGAAACTGAGAAGAAACGGTTTCAGAACGGGAATCCGGTTGACAACTCACGTTTTAGTCAATCTGAAAAGATTGGACATGATGCTGTGGTGAATACAATGGACACGGATGGAAATCAAGCCTCTAAAGTGTCGAGTGATGGATCTGGCAAAGTCGGGAAATTGGAGTTCGGATCGGGAATTAACGCGAGAGAATCTCAGAGCTCGCAACCAGTATTTTCAGATACCAGTGATGGTTTAGTTGAAAATTCAAGCAACACAGGCCACAAGCCACAAAGACAAATAGGCCGACTGAATATAAATTCTATTTTTGCCAATGCTAACGACAAGGAAAGTGGAAAAGCAGACAAAGAAAAGGACAATAATTCCGTGTTCAGTAAAAATAAAGCAGTTTTGATCAGAAGCCAAAGAAAACGCAAGGGAAGCAAGATAAAATCTGAGAGAGATGAAGAGCTAGCGAACCTCAGTCCTGAGGGTGAAGTGCCGTCGAATATGTCAGCAAATATGAAGCTTCAACTGGAAAAGATCCTGCAACAACGTTCAGCTTCGGTATCAAGCCAAGGTTCGTTGGTTTCTCCGAAGAACGACGGTAGAGAGAGCAGCTCTAGTCGGCTGTCTATATCAAGTGTATCGTCAGGTGGGTCGCCGAGATTTCGAGGCTCTTTCTCCAGTGATAGTAATCTCCTCAGGTATACCAGTTACGAAGAAAGCGACAATGGCGACGACCAAGGCCCAAAGAAGGTCAATAACGGTAGCCTGAAGTTCCAGCTGGATGGGATATTTCAAGCCAGGGTGCCAGGGAGTGGAAGTGTGGAGTCAAGCCCTGCCAACTCGCTCGACGCTTCTTTGAATTCCGAGGGCTTTGATGACTCGGACTTGTCAGAGAGAAAACCGAGTGTGGAAGACGATAGGAAAGACAAGCGAAAATTGATTGCAGACGCGATTAAGCTTAAGTACGGTGGAAAACTGGGTGGCGAAAAAAGAgataatagagaggatggtggagaaagagatgacaaaGACGACAGCGAAGCAAAGAGCGTGAAGGACTACGATAAAGGCGACAAAGGTTCCGAAAACACGGCAAAGCAGTTTATCAGCGAAAATGATATAGGGATTACAGCTGATTCTGATATGATGGGTAGCATGAATGCTAGACAAGGGAATAGAAGCTGGAAGGGTACATCAGATCGCCCTGGAGACAAAGAGACTCCATCTGTGCCGAATTCTCAGGAGTATAAATCAACTGAGGCTGATGGGCGGGGTGGATACGATCAAGAAAACAAAAGTTTAGAGAATGCTAAGAGGAGAGGAAAAGTTTCTATTCCGGGGATATTTTCAGGAATGCCAGACGCTGGGATTAGAGATAAAGAAACAGGGAATGCAGAACATAGAGCAAGAAGTGCTACACTGAAAGGAGGCCAACCCGAGATGGCTACCAGCAGATATGAAGAGACAGGAACTAGATGCAAAGAGTTGCCCAGAGAGGATAGCACGGAGAAAAAGGAAAGAGTCAACGTAGGAATAAGAAAGTTGAACATCCCTTCAAATTTTCAGACGAATTCAGCGGCCCGGAAaagtggtgatggtgatgacaatAACAGTCGGCCTAAGGCAGTAAGCTTCATGCAGAAATCAGCGGAAAGCAATGATTTGATGAACGGGAAAAAGACTGAACATCCGCAGGACTTGAATCAGGTGACGGGAGGCATTGCTAGAGAAAGTATTGAGCGAGTCAAGAATTCTGATGAGATAAAGGAAGATAATGCAAACGAGGAAACACGCAGAAAACCTGCGGGTAAACTGTCATCCTCGTTGTTTCAAGCGTTTCAGAGAAATGATAAGGAAAGCACAGGTGAGAAATTGTCAGGCGGGAATTCATCCAAAGCCACTGGCGTCAGAGCAAGCAATAACAGTTCTTCAGGGAAGTTAGCATCGCAGGCTCATGGCCAGTCTTCCGTTCATGATACAGTTAGCAGGATGAAAGAGATATCTACAGAAAACGAGGCAATGTCACGTGGTATAGACACGCCTGTGCAAGTTGAGAAAGAAGATGGGAGACATGGGAACGAcggcaacagcaacaacaacaacagccacagcaacaacaacaacaacaacgaagatgcaaacaacgacaacaacaacaacgacgacAACAACAACGAAGATGACAAATATAACAACAAGAAAGGTATCGGATTCGAGGCTAAAACAAAATGGCAGAGTCAGCAATCTTTCAAACAAGATCAATTGCAACCTTCAACAGAAGTAGTAGTTTCTAGCAAAAGGACAGTTGGAAAACTTAACATTCCACTTGCATTTAAATAA

Transcript

evm.model.HiC_scaffold_32.210

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q92540	Nonsense-mediated mRNA decay factor SMG7 OS=Homo sapiens OX=9606 GN=SMG7 PE=1 SV=2
Q5RJH6	Nonsense-mediated mRNA decay factor SMG7 OS=Mus musculus OX=10090 GN=Smg7 PE=2 SV=1
Q1LVF3	Nonsense-mediated mRNA decay factor SMG7 OS=Danio rerio OX=7955 GN=smg7 PE=2 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005919 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF10374 all species →	EST1	Telomerase activating protein Est1	Repeat	Interproscan
PF10373 all species →	EST1_DNA_bind	Est1 DNA/RNA binding domain	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR019458 all species →	Domain	Telomerase activating protein Est1-like, N-terminal	Interproscan
IPR045153 all species →	Family	Est1/Ebs1-like	Interproscan
IPR011990 all species →	Homologous_superfamily	Tetratricopeptide-like helical domain superfamily	Interproscan
IPR018834 all species →	Domain	DNA/RNA-binding domain, Est1-type	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR15696 all species →	SMG-7 SUPPRESSOR WITH MORPHOLOGICAL EFFECT ON GENITALIA PROTEIN 7	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000184 all species →	Biological Process	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	Interproscan
GO:0005697 all species →	Cellular Component	telomerase holoenzyme complex	Interproscan
GO:0042162 all species →	Molecular Function	telomeric DNA binding	Interproscan
GO:0070034 all species →	Molecular Function	telomerase RNA binding	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan

Search by domain instead of by gene. Any accession above (InterPro, Pfam, PANTHER, GO, KEGG) can be used as a query on the Functional Domain Search page, which searches all 148 annotated genomes at once.

KEGG pathway

No KEGG orthology assignment for evm.model.HiC_scaffold_32.210.

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Co-expression network

Genes whose expression across the transcriptome samples of Chrysaora quinquecirrha tracks this one. Counts are over the whole network; the network view itself draws at most 100 partners per query gene (CNIDO_NET_TOP_K), so a hub gene can show fewer edges than the number below.

No co-expression network has been built for this species, so this gene has no partners to show. Networks are available for the species listed on the Network Analysis page.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Chrysaora quinquecirrha, and in which cell types it is a marker. Expression is stored per cell, so the violin plot and the cell-type means are computed in the viewer — open a dataset to see them.

No single-cell dataset has been published for this species. The atlases that do exist are listed in the Cell Atlas.

Epigenetic marks

Chromatin and DNA-methylation data covering this gene. Peak calls are listed per sample with the genomic region the peak falls in; DNA methylation is listed as sample availability only, because those tables are queried by the DNA Methylation page itself.

No epigenomic data has been deposited for this species. The assays that exist across the site are described in the Epigenomic Data module.

What you can do with this gene

Every tool below opens with this gene already entered, so you land on the analysis rather than on an empty form. Links open in a new tab.

Analysis	What it does	Status
Primer design	Design PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.	template found	open →
BLAST	Search this gene’s sequence against the CnidoSite BLAST databases. The query is filled in and the species’ database is preselected — press Run to start.	template found	open →
Expression heatmap	Draw this gene’s expression as a heatmap across all RNA-seq samples, and compare it with the genes you add next to it.	no expression matrix	–
Gene family / orthogroup	Look this gene up in the single-copy orthogroups built from the high-quality cnidarian genomes, and see which other species carry an orthologue.		open →
Gene set analysis	Start a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.		open →